[3dem] Cryo-EM structures sought for CASP13

[Cathy Lawson]

Critical Assessment of Techniques for Protein Structure Prediction (CASP 
<http://www.predictioncenter.org>) community experiments aim to advance 
the state of the art in protein structure modeling. Every other year 
since 1994, CASP collects information on soon-to-be released 
experimental structures, passes on sequence data to the structure 
modeling community, and collects blind predictions of structure for 
assessment. About 100 modeling groups from around the world participate. 
Results of CASP experiments are published in special issues of the 
journal PROTEINS (e.g., CASP12: Proteins Vol 86, Issue S1, March 2018 
<https://onlinelibrary.wiley.com/toc/10970134/86/S1>).

The thirteenth CASP round is scheduled to start on May 1, 2018. /The 
organizing committee is particularly keen to include many 
cryo-EM-derived structure targets in this round./

The success of CASP depends on the generosity of the structure 
determination community. Modeling targets are needed over a wide range 
of difficulty, for modeling both with and without the aid of templates. 
Targets that can be modeled based on structural templates should ideally 
have 50% or less sequence identity to the templates. Access to the 
structure in advance of its release by the PDB or its publication is not 
needed. With sufficient notification to CASP (a minimum of three weeks 
before release, more is better) there is no need to delay structure 
release. If you have recently determined a novel protein structure and 
will be depositing it to PDB, please suggest it as a target for CASP by 
visiting www.predictioncenter.org/casp13/targets_submission.cgi 
<http://www.predictioncenter.org/casp13/targets_submission.cgi>. If you 
have any questions please contact casp at predictioncenter.org 
<mailto:casp at predictioncenter.org>.

CASP target providers are regularly invited to contribute to special 
issue papers, for example:

  * 2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT,
    Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F,
    Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC,
    Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M,
    Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D,
    Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A,
    Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target
    highlights from the first post-PSI CASP experiment (CASP12,
    May-August 2016). Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392
    <http://dx.doi.org/10.1002/prot.25392>. PMID: 2896053
  * 2016: 
Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK,
    Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D,
    Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij
    MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson
    MA, Schwede T. (2016). Some of the most interesting CASP11 targets
    through the eyes of their authors. Proteins 84 (S1), 34-50. doi:
    10.1002/prot.24942 <http://dx.doi.org/10.1002/prot.24942>. PMID:
    26473983
  * 2014: Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin
    A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C,
    Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ,
    Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. (2014).
    Challenging the state-of-the-art in protein structure prediction:
    Highlights of experimental target structures for the 10th critical
    assessment of techniques for protein structure prediction experiment
    CASP10. Proteins 82 (S2), 26-42. doi: 10.1002/prot.24489
    <http://dx.doi.org/10.1002/prot.24489>. PMID: 2431898
  * 2011: Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H,
    Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T,
    Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA,
    Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A,
    Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont
    AK, Young J, Schwede T. (2011). Target highlights in CASP9:
    Experimental target structures for the critical assessment of
    techniques for protein structure prediction. Proteins 79 (S10),
    6-20. doi: 10.1002/prot.23196
    <http://dx.doi.org/10.1002/prot.23196>. PMID: 2202078

Posted on behalf of the CASP organizing committee:
John Moult, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis USA
Torsten Schwede, University of Basel, Switzerland

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20180328/311eb646/attachment.html>